To find the secret crypt in Via Veritas in Mission of San Juan in Shadow of the Tomb Raider go up the stairs and to the back left of the room and destroy the wall. Go back down stairs and up to the wall further down on the same side as the entrance. Go up the the large wall at the front of the room. To find the cross turn around and go to the back of the library.
The cross is in the wall ahead. .
As found on Youtube